Case Report: Evolution of Humoral and Cellular Immunity in Two COVID-19 Breakthrough Infections After BNT162b2 Vaccine

Abstract

Background: SARS-CoV-2 breakthrough infections after complete vaccination are increasing whereas their determinants remain uncharacterized.

Methods: We analyzed two cases of post-vaccination SARS-CoV-2 infections by α and β variants, respectively. For each participant both humoral (binding and neutralizing antibodies) and cellular (activation markers and cytokine expression) immune responses were characterized longitudinally.

Results: The first participant (P1) was infected by an α variant and displayed an extended and short period of viral excretion and symptom. Analysis of cellular and humoral response 72 h post-symptom onset revealed that P1 failed at developing neutralizing antibodies and a potent CD4 memory response (lack of SARS-CoV-2 specific CD4⁺IL-2⁺ cells) and CD8 effector response (CD8⁺IFNγ⁺ cells). The second participant (P2) developed post-vaccination SARS-CoV-2 infection by a β variant, associated with a short period of viral excretion and symptoms. Despite displaying initially high levels and polyfunctional T cell responses, P2 lacked initial β-directed neutralizing antibodies. Both participants developed and/or increased their neutralization activity and cellular responses against all variants, namely, β and δ variants that lasts up to 3 months after breakthrough infection.

Conclusions: An analysis of cellular and humoral response suggests two possible mechanisms of breakthrough infection: a poor immune response to vaccine and viral evasion to neutralizing antibodies.

Keywords: SARS-CoV-2; breakthrough infection; immune evasion; vaccine; variant of concern.

Figure 1

Longitudinal follow-up of anti-SARS-CoV-2 humoral response after breakthrough infection in patient 1 (P1) and patient 2 (P2). (A) Viral shedding and antibodies detected against the SARS-CoV-2 spike (S) protein in nasopharyngeal swabs from P1 (red dots) and P2 (blue dots). Ct values are depicted on the first graph (left) and anti-S IgA and IgG levels on the two other graphs. to the positivity threshold. (B) Antibodies directed against SARS-CoV-2 receptor binding domain (RBD), S or nucleocapsid (N) proteins measured in serum from P1 (red dots) and P2 (blue dots). (C, D) Half-maximal inhibitory concentration (IC₅₀) measured in P1 (C) and P2 (D) by pseudoparticle-based (left) and live-virus neutralization (right) assays against several SARS-CoV-2 variants. Sera displaying less than 50% luminometric signal reduction relative to the control condition with the first serum dilution tested (1:40 and 1:30 with pseudoparticle-based and live-virus neutralization assays, respectively) were considered negative and depicted on graphs with an IC₅₀ set arbitrarily at 20. The dotted horizontal black lines correspond to positivity thresholds. BAU, Binding Antibody Units; BU, binding units; Ct, Cycle threshold.

Figure 2

Characterization of anti-SARS-CoV-2 cellular response after breakthrough infection in patient 1 (P1) and patient 2 (P2). (A) T-cell reactivity measured by IFN-γ ELISPOT against the N-terminal (S1) and C-terminal (S2) parts of the SARS-CoV-2 spike protein from wild-type strain and α and β variants. Bar charts and error bars represent mean positive values and standard deviations of spot counts per million of peripheral blood mononuclear cells (PBMCs). (B) Dot plots showing examples of AIM⁺ and cytokine⁺ cells after stimulation with S1 α peptide pools on the early infection time points for P1 (first row) and P2 (second row). From left to right, dot plots depict, CD4⁺AIM⁺, CD8⁺AIM⁺, CD4⁺TNFα⁺, CD8⁺TNFα⁺, CD4⁺IL-2⁺ and CD8⁺IFNγ⁺ cells. (C) Bar charts representing AIM⁺ and cytokine⁺ cells frequencies for each T cell subset (either CD4 or CD8). Results are displayed for each variant (wild type, α and β) and each SARS-CoV-2 part (S1 and S2). The color code is as follows: P1 at 3 days (red) and 85 days (orange) and from P2 at 4 days (dark blue) and 91 days (light blue) after symptom onset.